SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Variant calling with GATK between two cell lines ErikFas Bioinformatics 0 07-02-2015 02:34 AM
GATK Based Variant calling STEPS satishkumar Bioinformatics 1 10-23-2014 09:21 PM
GATK variant calling statistics... milesgr Bioinformatics 1 01-23-2014 10:01 AM
Problems using GATK for variant calling pooja_singh RNA Sequencing 1 07-07-2012 11:23 AM
GATK variant calling for multiple exome sehrrot Bioinformatics 2 04-24-2012 05:09 AM

Reply
 
Thread Tools
Old 09-08-2015, 09:04 AM   #1
NikTuzov
Registered Vendor
 
Location: Illinois, USA

Join Date: Mar 2013
Posts: 18
Default Using GATK's local realigner outside of GATK pipeline for variant calling

Hello all:

If I were to use GATK's local realigner outside of GATK pipeline, eg:

BWA -> GATK's Local Realigner -> SAMTools

then will I have any extra problems because I use non-GATK modules upstream or downstream of realignment?

Thanks,
Nik
NikTuzov is offline   Reply With Quote
Old 09-08-2015, 09:41 AM   #2
HESmith
Senior Member
 
Location: Bethesda MD

Join Date: Oct 2009
Posts: 499
Default

No problem - in fact, the latest version of SAMtools variant-calling workflow uses GATK's realigner and base recalibrator.

Last edited by HESmith; 09-08-2015 at 12:22 PM. Reason: typo
HESmith is offline   Reply With Quote
Reply

Tags
gatk indelrealigner, samtools, variant detection

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:49 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO